Scanning tunneling microscopy (STM) studies have demonstrated that monolayer-deep, flat-bottomed, circular etch pits can be grown on highly ordered pyrolytic graphite by high-temperature etching in the presence of oxygen. In this work, these graphite etch pits are used as "molecule corrals" to isolate ensembles of molecules for study by STM. The nucleation of self-assembled molecular films in the corrals took place by nucleation events separate from those leading to self-assembly on the surrounding terrace and allowed the measurement of the nucleation rate constant in the corrals. The dependence of the nucleation rate for self-assembly on pit size shows that nucleation occurs at open terrace sites and that step edges (that is, the corral’s perimeter) and confinement inhibit film growth.